From 223ccb5ee354120aa99f3f8887a9d094267f6546 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 4 May 2017 14:03:42 +0100
Subject: [PATCH] JAL-2507 JAL-2509 allow differences in visibility of
 annotation rows to be ignored when comparing round-tripped
 alignments

---
 test/jalview/io/StockholmFileTest.java |   36 ++++++++++++++++++++++++++++----
 1 file changed, 32 insertions(+), 4 deletions(-)

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index e9edd1b..e7f1435 100644
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -56,7 +56,8 @@ public class StockholmFileTest
   @Test(groups = { "Functional" })
   public void pfamFileIO() throws Exception
   {
-    testFileIOwithFormat(new File(PfamFile), FileFormat.Stockholm, -1, 0);
+    testFileIOwithFormat(new File(PfamFile), FileFormat.Stockholm, -1, 0,
+            false);
   }
 
   @Test(groups = { "Functional" })
@@ -81,7 +82,8 @@ public class StockholmFileTest
   @Test(groups = { "Functional" })
   public void rfamFileIO() throws Exception
   {
-    testFileIOwithFormat(new File(RfamFile), FileFormat.Stockholm, 2, 1);
+    testFileIOwithFormat(new File(RfamFile), FileFormat.Stockholm, 2, 1,
+            false);
   }
 
   /**
@@ -93,10 +95,11 @@ public class StockholmFileTest
    * @param ioformat
    *          - label for IO class used to write and read back in the data from
    *          f
+   * @param ignoreRowVisibility
    */
 
   public static void testFileIOwithFormat(File f, FileFormatI ioformat,
-          int naliannot, int nminseqann)
+          int naliannot, int nminseqann, boolean ignoreRowVisibility)
   {
     System.out.println("Reading file: " + f);
     String ff = f.getPath();
@@ -174,6 +177,27 @@ public class StockholmFileTest
   public static void testAlignmentEquivalence(AlignmentI al,
           AlignmentI al_input, boolean ignoreFeatures)
   {
+  }
+
+  /**
+   * assert alignment equivalence
+   * 
+   * @param al
+   *          'original'
+   * @param al_input
+   *          'secondary' or generated alignment from some datapreserving
+   *          transformation
+   * @param ignoreFeatures
+   *          when true, differences in sequence feature annotation are ignored
+   * 
+   * @param ignoreRowVisibility
+   *          when true, do not fail if there are differences in the visibility
+   *          of annotation rows
+   */
+  public static void testAlignmentEquivalence(AlignmentI al,
+          AlignmentI al_input, boolean ignoreFeatures,
+          boolean ignoreRowVisibility)
+  {
     assertNotNull("Original alignment was null", al);
     assertNotNull("Generated alignment was null", al_input);
 
@@ -207,8 +231,12 @@ public class StockholmFileTest
           // compare graphGroup or graph properties - needed to verify JAL-1299
           assertEquals("Graph type not identical.", aa_original[i].graph,
                   aa_new[i].graph);
-          assertEquals("Visibility not identical.", aa_original[i].visible,
+          if (!ignoreRowVisibility)
+          {
+            assertEquals("Visibility not identical.",
+                    aa_original[i].visible,
                   aa_new[i].visible);
+          }
           assertEquals("Threshold line not identical.",
                   aa_original[i].threshold, aa_new[i].threshold);
           // graphGroup may differ, but pattern should be the same
-- 
1.7.10.2